Mogul - a knowledge base of molecular geometry
Mogul provides easy access to information on the preferred values of
bond lengths, valence angles and acyclic torsion angles, using data
derived from the CSD.
Given the instruction to retrieve data for a particular geometric
feature in an input molecule, e.g. a valence angle, Mogul will
automatically generate atom and bond-based keys that describe the
environment of that feature. These keys are then used to retrieve all
CSD entries that contain the feature of interest.
Resulting statistics, such as the mean and median valence-angle values can then be displayed interactively in the graphical interface or passed via an ASCII file interface to other programs.
Results and Analysis
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View Structures
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Potential Applications:
- Validation of newly determined crystal structures (and identification of unusual geometrical features)
- In protein-ligand docking, filtering out ligands that have been docked with unlikely torsion angles
- The setting up of ligand dictionaries for protein crystal structure refinement
- Facilitating the solution of structures from powder diffraction data
Features:
- Rapid access to bond lengths, valence angles and acyclic torsions in the CSD
- Generation and optional assignment of bond type information and hydrogen atoms if missing from the input structure
- An intuitive sketcher for generation of user-defined molecules in 2D
- A graphical interface allowing inspection of bond-length, angle and torsion histograms, with selection/deselection of histogram bars and mviewing of crystal structures contributing to the histogram
- The ability to load files in a number of formats (e.g. MOL2, CIF, RES, MOL/SD, PDB) into the Mogul graphical interface
- A command-line interface which can be used to initiate Mogul searches for all bond lengths, angles and torsions in a molecule, with results (mean values, standard deviations, etc.) being written to an output file to facilitate integration with other applications
- Filtering on experimental precision
- The ability to find structurally related entries if insufficient hits are retrieved
For further details follow the link to the Cambridge site at the head
of the page.
To use Mogul you need access to a system with X-Windows graphics and a
reasonably good network connection to the CDS server. If you have set
up your system to access to ConQuest you should be able to use Mogul
(logon to the CDS server and type "mogul" at the prompt).
If you encounter any problems contact cdsbb@stfc.ac.uk.